It seems that during Anne's first couple of days in the Tower, her ramblings and hysterics led to the mention of Sir Francis Weston, whom she claimed was in love with her. Anne supposedly said this to one of her attendants, Mrs. Coffin, and insisted that Weston had flirted with the Queen's cousin Lady Shelton, only to be reprimanded by the Queen herself, seeing as Lady Shelton was betrothed to Sir Henry Norris. When Anne wondered aloud why Norris would not get on with the marriage, Weston replied "came more to her chamber for her than for Madge." It's unclear whether Weston was referring to himself or to Norris, but either way when Anne told Mrs. Coffin, the story travelled quickly to Thomas Cromwell - (Mrs. Coffin had evidently been a spy). Thus, Weston was arrested and hauled to the Tower, where he would remain until 17 May, and would be beheaded on the treasonous charges of adultery with the Queen and plotting to kill the King - although there has been no evidence found that these accusations were true. If you watched The Tudors, you may remember that Sir Francis Weston was mysteriously absent and was not portrayed. I do not know the reason for this, but I suppose he was a rather unsubstantial figure.
Firstly, Cromwell accused that Anne had solicited Brereton on 16 November 1533, and that their adultery took place on 27 November. This is actually extremely unlikely, seeing as Anne had just given birth to Princess Elizabeth on 7 September 1533, and therefore would have still been in seclusion for a few months. Also, the allegations were that Brereton and the Queen had committed adultery at Hampton Court Palace, when in fact Anne and the rest of the court would have been at Greenwich at that time, since that is the palace where Princess Elizabeth was born.
So, these charges were not very well-thought out, and it is true that they make little sense, but in any case Brereton was arrested, and it has been suggested by historian Eric Ives that Cromwell simply wanted to reorganize and centralize the government and remove Brereton because of the trouble he was causing (and the wealth he was gaining) in the Welsh Marches.
Most historians can agree that Weston and Brereton (as well as the other men accused) were all innocent, but they would suffer greatly anyway - They would all be beheaded a the Tower of London on 17 May 1536, two days before Queen Anne.